Multiple-locus variable-number tandem repeat analysis, a novel typing scheme to study the genetic relatedness and epidemiology of Enterococcus faecium isolates - PubMed (original) (raw)

Multiple-locus variable-number tandem repeat analysis, a novel typing scheme to study the genetic relatedness and epidemiology of Enterococcus faecium isolates

Janetta Top et al. J Clin Microbiol. 2004 Oct.

Abstract

Multiresistant Enterococcus faecium is a major cause of hospital acquired infections and outbreaks. Here, we describe the development of multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) as a novel typing method to assess the genetic relatedness of E. faecium isolates. Six VNTR loci were used to genotype 392 isolates recovered from different animals and human community, hospital survey, and clinical isolates. From 3 to 13 alleles were found per locus, resulting in 127 different MLVA profiles. Clustering of MLVA profiles confirmed the host-specific genogroups found by multilocus sequence typing (MLST) and showed the grouping of clinical and epidemic isolates that belonged to the MLST-C1 cluster in a distinct MLVA-C1 cluster (sensitivity of 97% and specificity of 90%). Furthermore, the discriminatory power of MLVA is comparable to MLST. MLVA profiles appeared to be relatively stable, since isolates from a single outbreak shared the same MLVA profile, which is a prerequisite when MLVA is used to study hospital outbreaks. Our data show that MLVA is a highly reproducible and portable typing method; in contrast to MLST, it is fast, relatively cheap, and easy to perform. Furthermore, it has the abilities of MLST to recognize genetically related and potential epidemic isolates. Submission of MLVA profiles is possible via a Web-based database for international comparison.

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Figures

FIG. 1.

FIG. 1.

UPGMA clustering of the 127 different MLVA profiles with a categorical similarity coefficient. For each MT, the number of isolates, MLST sequence types, MLST and AFLP genogroups, and MLVA profile are depicted. C1, epidemic isolates (24 of 25 isolates); C and C1, clinical infection (102 of 126 isolates); B, calf (19 of 19 isolates) and poultry (13 of 13 isolates); A, community survey (12 of 17 isolates) and pigs (16 of 20 isolates). A (17 isolates), B (7 isolates), C (17 isolates), and C1 (24 of 68 isolates), hospital survey; R, miscellaneous origin.

FIG. 1.

FIG. 1.

UPGMA clustering of the 127 different MLVA profiles with a categorical similarity coefficient. For each MT, the number of isolates, MLST sequence types, MLST and AFLP genogroups, and MLVA profile are depicted. C1, epidemic isolates (24 of 25 isolates); C and C1, clinical infection (102 of 126 isolates); B, calf (19 of 19 isolates) and poultry (13 of 13 isolates); A, community survey (12 of 17 isolates) and pigs (16 of 20 isolates). A (17 isolates), B (7 isolates), C (17 isolates), and C1 (24 of 68 isolates), hospital survey; R, miscellaneous origin.

FIG. 2.

FIG. 2.

eBURST clustering of the 127 different MLVA profiles. In the eBURST algorithm, each MT is represented as a node (solid black dot). For clarity, only clusters or clonal complexes of related MTs are depicted. Dark-gray dot, primary founder. Light-gray dots, subgroups or secondary founders. The clinical relevant genogroup MLVA-C1 based on the UPGMA clustering is surrounded with a dotted circle.

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